Estimating evolutionary distances between genomic sequences from spaced-word matches.
Identifieur interne : 000087 ( France/Analysis ); précédent : 000086; suivant : 000088Estimating evolutionary distances between genomic sequences from spaced-word matches.
Auteurs : Burkhard Morgenstern [France] ; Bingyao Zhu [Allemagne] ; Sebastian Horwege [Allemagne] ; Chris André Leimeister [Allemagne]Source :
- Algorithms for molecular biology : AMB [ 1748-7188 ] ; 2015.
Abstract
Alignment-free methods are increasingly used to calculate evolutionary distances between DNA and protein sequences as a basis of phylogeny reconstruction. Most of these methods, however, use heuristic distance functions that are not based on any explicit model of molecular evolution. Herein, we propose a simple estimator d N of the evolutionary distance between two DNA sequences that is calculated from the number N of (spaced) word matches between them. We show that this distance function is more accurate than other distance measures that are used by alignment-free methods. In addition, we calculate the variance of the normalized number N of (spaced) word matches. We show that the variance of N is smaller for spaced words than for contiguous words, and that the variance is further reduced if our spaced-words approach is used with multiple patterns of 'match positions' and 'don't care positions'. Our software is available online and as downloadable source code at: http://spaced.gobics.de/.
DOI: 10.1186/s13015-015-0032-x
PubMed: 25685176
Affiliations:
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